I would like to use either Hyper-V or Vmware to take a Clean Base snapshot and a snapshot after an application or virus has made changes so I can then see what was changed between the two images.

VMware ThinApp is the closest thing I can find to this as it shows what was modified between the 2 images as it is trying to create a Virtualized Application. I am not interested in making an virtualized application, I have been using the power of the application to determine other items but would like to know if there are better programs and tools for this type of work.

I do know that some virus can detect being ran inside a VM and will not execute.

Just a quick hint, you can always use a hardware machine and make a binary copy of the hard drive. both Both copies will need to be compared. You can do this by running a checksum. Just be sure nothing is run from the hard drive.

I think backtrack has a nice toolset to do such analysis. You can find them under digital forensics.